Development of PCR-based SCAR and CAPS markers linked to β-glucan and protein content QTL regions in oat

A key breeding objective in oat (Avena sativa L.) is cultivars with high and low β-glucan content. In a targeted strategy to develop PCR-based markers linked to published β-glucan content quantitative trait loci (QTLs) regions, 15 random amplified polymorphic DNA (RAPD) fragments were cloned and their sequences used to design sequence-characterized amplified region (SCAR) and cleaved amplified polymorphic sequence (CAPS) primers. The 13 derived SCAR markers and 2 derived CAPS markers were mapped on either the ‘Kanota’ × ‘Ogle’ (KO) or the ‘Terra’ × ‘Marion’ (TM) oat reference map. In addition, 3 previously reported SCAR markers were characterized further. Ten SCAR markers and one CAPS marker were associated with β-glucan QTL regions and many of these are also associated with QTLs for protein content or other traits. These markers have the potential to help define homologous and homoeologous relationships in oat and investigate the complex genetics of β-glucan and protein content.